Lec 03_ Protein Structure and Function

Protein Structure and Function

• Proteins are essential molecules in biological systems, playing various roles including acting as enzymes.

Amino Acids

• Proteins are composed of 20 different amino acids.

• Amino acids are linked together by covalent peptide bonds forming long chains called polypeptides.

• The specific sequence of amino acids defines the unique structure and function of each protein.

Polypeptides

• Polypeptides have a backbone made of repeating core atoms: -N-C-C-.

• They exhibit directionality:

  • Amino terminus (N-terminus) - free amino group end.

  • Carboxyl terminus (C-terminus) - free carboxyl group end.

Side Chains

• Side chains extend from the backbone and determine the unique properties of each amino acid.

  • Types include:

    • Nonpolar and hydrophobic

    • Charged (positive or negative)

    • Chemically reactive

• Examples of amino acids with specific properties:

  • Charged: Arginine (Arg), Histidine (His), Lysine (Lys)

  • Polar Uncharged: Serine (Ser), Threonine (Thr), Glutamine (Gln), Asparagine (Asn)

  • Negative: Aspartic Acid (Asp), Glutamic Acid (Glu)

  • Hydrophobic: Methionine (Met), Phenylalanine (Phe), Isoleucine (Ile), Leucine (Leu)

Shaping a Protein

• Peptide bonds allow flexible rotation, providing flexibility to polypeptide chains.

• Noncovalent interactions (hydrogen bonds, electrostatic attractions, van der Waals forces) are crucial for protein folding.

• Hydrophobic interactions lead to compact protein shapes.

Protein Folding

• Proteins fold into their lowest energy (most stable) conformation.

• Folding may allow some proteins to regain their structure if they become denatured, given appropriate conditions.

Chaperone Proteins

• Chaperones assist in the correct folding of newly synthesized polypeptides, often requiring ATP energy.

• Some act as isolated chambers to help proteins fold properly.

Folding Patterns

• Proteins commonly adopt two structures:

  • α Helix: spiral structure formed by hydrogen bonds.

  • β Sheet (or β-pleated sheet): formed through hydrogen bonds between segments of polypeptide chains.

Levels of Organization

• Protein structure levels include:

  • Primary: Amino acid sequence.

  • Secondary: Local structures like α helices and β sheets.

  • Tertiary: Three-dimensional conformation of the entire polypeptide chain.

  • Quaternary: Complex formed by multiple polypeptide chains.

Protein Domains

• Protein domain: independently folding segment of a polypeptide, often distinct from the main structure.

• Includes intrinsically disordered segments that lack defined structures.

Protein Families

• Groups of similar proteins with analogous amino acid sequences and structures, e.g., serine proteases.

Larger Proteins

• Can contain multiple subunits, where each subunit may have independent folding regions or domains.

Other Protein Shapes

• **Globular Proteins:**Compact, spherical shapes (e.g., enzymes).

• Fibrous Proteins: Long, elongated structures (e.g., keratin).

Stabilization by Covalent Cross-Linkages

• Proteins in cells often stabilized by covalent bonds like disulfide bonds (formed from cysteine side chains) for structural integrity.

Protein Binding

• Proteins bind specificity to molecules (ligands) through binding sites, affecting their biological function.

Antibodies

• Specialized immunoglobulin proteins that bind to foreign molecules (antigens) with high specificity, crucial for immune response.

Enzymes

• Catalysts for biochemical reactions, converting substrates into products, and significantly speeding up reaction rates.

Lysozymes

• Enzymes with antibiotic functions; they break down bacterial cell walls by hydrolyzing polysaccharide chains.

Enzyme-Substrate Complex

• ES Complex functions:

  • Holds substrate in orientation close to the transition state.

  • Alters local environment to favor reactions.

  • Strains bound substrates to facilitate transitions.

Regulation of Protein Activity

• Gene expression and degradation regulate protein quantity.

• Enzymatic activities can be compartmentalized within cells.

• Proteins can be activated or inactivated by conformational changes.

Feedback Inhibition

• Occurs when a product inhibits an enzyme in a metabolic pathway, providing negative feedback regulation.

• Also involves positive regulation enhancing enzyme function.

Allosteric Enzymes

• Enzymes with multiple binding sites; their activity is regulated by conformational changes due to molecule binding.

Phosphorylation

• Addition of phosphate groups alters protein conformation and activity; regulated by kinases (addition) and phosphatases (removal).

GTP-Binding Proteins

• Act as molecular switches. Active when GTP is bound; hydrolyze GTP to GDP to become inactive.

Motor Proteins

• Drive cellular movements, including muscle contractions.

Protein Machines

• Multi-protein complexes that perform essential cellular processes through coordinated activities.

Purifying Proteins

• The process involves breaking cells, fractionating, and using chromatography techniques for purification based on protein properties.

Determining Protein Structure

• Involves sequencing amino acids and analyzing fragments through classical methods or mass spectrometry.

Predicting Conformation

• Currently requires experimentation (e.g., X-ray crystallography, NMR) as the precise structure cannot be predicted solely from sequence.